Comprehensive Genome Analysis Service

Overview

The Comprehensive Genome Analysis Service provides a streamlined analysis “meta-service” that accepts raw reads and performs a comprehensive analysis including assembly, annotation, identification of nearest neighbors, a basic comparative analysis that includes a subsystem summary, phylogenetic tree, and the features that distinguish the genome from its nearest neighbors.

Using the Comprehensive Genome Analysis Service

The Comprehensive Genome Analysis submenu option under the Services main menu (Genomics category) opens the Comprehensive Genome Analysis input form (shown below). Note: You must be logged into PATRIC to use this service.

../../_images/services_menu.pngComprehensive Genome Analysis Menu

Options

../../_images/genome_analysis_input_form.pngComprehensive Genome Analysis Input Form

Start with

The service can accept either read files or assembled contigs. If the “Read Files” option is selected, the Assembly Service will be invoked automatically to assemble the reads into contigs before invoking the Annotation Service. If the “Assembled Contigs” option is chosen, the Annotation Service will automatically be invoked, bypassing the Assembly Service.

Read Input File

Depending on the option chosen above (Read File or Assembled Contigs), the Input File section will request read files or assembled contigs, respectively.

Paired read library

Read File 1 & 2: Many paired read libraries are given as file pairs, with each file containing half of each read pair. Paired read files are expected to be sorted such that each read in a pair occurs in the same Nth position as its mate in their respective files. These files are specified as READ FILE 1 and READ FILE 2. For a given file pair, the selection of which file is READ 1 and which is READ 2 does not matter.

Single read library

Read File: The fastq file containing the reads.

SRA run accession

Allows direct upload of read files from the NCBI Sequence Read Archive to the PATRIC Assembly Service. Entering the SRR accession number and clicking the arrow will add the file to the selected libraries box for use in the assembly.

Selected libraries

Read files placed here will contribute to a single assembly.

Parameters

Assembly Strategy

Note: Available only when “Read File” is selected above.

auto

  • For short reads:
    1. Runs BayesHammer on reads
    2. Assembles with Velvet, IDBA and SPAdes
    3. Sorts assemblies by ARAST quality score
  • For long reads (PacBio or Nanopore):
    1. Assembles with MiniASM

fast

  1. Assembles with MEGAHIT and Velvet.
  2. Results are sorted by ARAST quality score.

full_spades

  1. Runs BayesHammer on reads
  2. Assembles with SPAdes.

kiki

  1. Runs the Kiki assembler

miseq

  1. Runs Velvet with hash length 35.
  2. Runs BayesHammer on reads and assembles with SPAdes with k up to 99.
  3. Results are sorted by ARAST quality score.
  4. Works for Illumina MiSeq reads.

plasmid

  1. Runs BayesHammer on reads and assembles with plasmidSPAdes.

smart

  • For short reads:
    1. Runs BayesHammer on reads, Kmergenie to choose hash-length for Velvet
    2. Assembles with Velvet, IDBA and SPAdes
    3. Sorts assemblies by ALE score
    4. Merges the two best assemblies with GAM-NGS
  • For long reads (PacBio or Nanopore):
    1. Assembles with MiniASM

Domain

The taxonomic domain of the target organism: bacteria or archaea.

Taxonomy Name

Taxon must be specified at the genus level or below to get the latest protein family predictions.

Taxonomy ID

Auto-populated after entering Taxonomy Name. If a Taxonomy ID is entered, auto-populates the Taxonomy Name

Genetic Code

The codon translation used in calling genes.

Output Folder

The workspace folder where results will be placed.

Output Name

Name used to uniquely identify results.

Output Results

../../_images/cga_service_output_files.pngComprehensive Genome Analysis Output Files

The Comprehensive Genome Analysis Service generates several files that are deposited in the Private Workspace in the designated Output Folder. These include

  • FullGenomeReport.html - A web-browser-viewable report that summarizes the results of the service including
    • Summary information - genome name, quality,
    • Genome assembly information - contigs, GC content, plasmids, L50, genome length, chromosomes
    • Genome annotation information - taxonomy, CDS, tRNA, rRNA, partial CDS, misc RNA, repeat regions, protein feature summary, circular view with annotations
    • Specialty genes - antibiotic resistance, drug targets, transporters, virulence factors
    • Subsystem analysis - summary
    • Phylogenetic analysis - phylogenetic tree generated using the analyzed genome and the closest Reference and Representative genomes
    • References - citations to all tools used by the service
  • annotated.genome - A special “Genome Typed Object (GTO)” JSON-format file that encapsulates all the data from the annotated genome. See Extracting and Mining Genome Typed Objects for more information.
  • annotation - The Annotation sub-job that was run as part of the CGA Service. Double-clicking this item will display the Annotation job results. Note that sub-jobs are indicated by the “checkered flag” icon beside the name.
  • assembly - The Assembly sub-job that was run as part of the CGA Service. Double-clicking this item will display the Assembly job results. Note that sub-jobs are indicated by the “checkered flag” icon beside the name.
  • circos.svg - SVG-format rendering of the circular genome view used in the FullGenomeReport.html file.
  • circos.png - PNG-format rendering of the circular genome view used in the FullGenomeReport.html file.
  • codonTree.nex - NEXUS-format file containing the phylogenetic tree generated by the CGA Service.
  • codonTree.nwk - Newick-format file containing the phylogenetic tree generated by the CGA Service.
  • codonTree.stats - File containing the statistics on the phylogenetic tree generated by the CGA Service.
  • codonTree.svg - SVG-format rendering of the phylogenetic tree used in the FullGenomeReport.html file.
  • subsystem_colors.json - JSON-format file used for rendering colors in the Subsystem pie chart displayed in the FullGenomeReport.html file.
  • tree_ingroup.txt - File containing the closely related genomes used in building the ingroup for the phylogenetic tree generated by the CGA Service.